Figure 1. Whole cell extract sequencing (WCEseq) libraries are biased by genomic copy.

The genome-wide copy number of MCF-7 (obtained from array CGH) at 1 Mbp resolution is contrasted to estimations made from (a) a WCEseq library and (b) ER ChIP-enriched library, sorted in chromosomal order. The high correlation (Pearson's r = 0.875) between WCEseq estimate and actual aCGH readout indicates coarse-scale profile of WCEseq library is dominantly shaped by copy number variations. Inherent effect of copy number variations also strongly affect ChIP-enriched library (Pearson's r = 0.673).